You are correct. APE is the culprit, and let me tell you it's very, very bad. Bad APE! I've tried Unsanity's haxies on and off over the years hoping that they'd work as promised but they never do and usually you end up with a borked system. I'll never install APE again because it causes so many problems.

Unfortunately ShapeShifter was part of the MacHeist bundle. It keeps coming back to try and haunt my Mac!